SMTL ID : 4c8e.1

IspF (Burkholderia cenocepacia) 2CMP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.31, H.33, H.65 Ligands: C5P.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.31, A:H.33, A:H.65, C5P.3 ZN.4: 4 residues within 4Å: Chain B: D.31, H.33, H.65 Ligands: C5P.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.31, B:D.31, B:H.33, B:H.65, C5P.6 ZN.8: 4 residues within 4Å: Chain C: D.31, H.33, H.65 Ligands: C5P.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.31, C:H.33, C:H.65, C5P.11

6 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.2: 12 residues within 4Å: Chain A: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 Chain C: D.79, G.81, R.82 Ligands: C5P.11 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:T.156 Hydrogen bonds: A:A.123, A:L.128, A:A.129, A:T.156, A:T.156, C:D.79, C:G.81, C:R.82 Water bridges: A:K.127, A:A.154, A:A.154, A:T.156, A:E.158, A:E.158, A:E.158 Salt bridges: A:K.155 C5P.3: 14 residues within 4Å: Chain A: D.31, H.33, H.57, S.58, H.65, I.80, G.81, F.84, A.94, D.95, L.99 Chain B: K.155 Ligands: ZN.1, C5P.5 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.99 Hydrogen bonds: A:H.57, A:S.58, A:A.94, B:E.158, B:E.158 Salt bridges: A:H.33, A:H.65, B:K.155 Water bridges: B:K.155, B:K.155, B:E.158 C5P.5: 13 residues within 4Å: Chain A: D.79, I.80, G.81, R.82 Chain B: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 Ligands: C5P.3 16 PLIP interactions: 6 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:D.79, A:G.81, A:R.82, B:A.123, B:L.128, B:A.129, B:T.156, B:T.156 Water bridges: A:D.31, A:D.31, A:V.32, B:A.154, B:T.156, B:E.158 Hydrophobic interactions: B:T.156 Salt bridges: B:K.155 C5P.6: 15 residues within 4Å: Chain B: D.31, H.33, H.57, S.58, H.65, I.80, G.81, F.84, D.86, A.94, D.95, L.99 Chain C: K.155 Ligands: ZN.4, C5P.10 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain B Water bridges: C:K.155, B:H.33 Salt bridges: C:K.155, B:H.33, B:H.65 Hydrophobic interactions: B:L.99 Hydrogen bonds: B:H.57, B:S.58, B:A.94 C5P.10: 13 residues within 4Å: Chain B: D.79, I.80, G.81, R.82 Chain C: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 Ligands: C5P.6 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:T.156 Hydrogen bonds: C:A.123, C:L.128, C:A.129, C:T.156, C:T.156, B:D.79, B:G.81, B:R.82 Water bridges: C:A.154, C:K.155, C:E.158, B:D.31, B:V.32 Salt bridges: C:K.155 pi-Cation interactions: C:K.127 C5P.11: 13 residues within 4Å: Chain A: K.155 Chain C: D.31, H.33, H.57, S.58, H.65, I.80, F.84, A.94, D.95, L.99 Ligands: C5P.2, ZN.8 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain C Water bridges: A:K.155, A:E.158, C:H.57 Salt bridges: A:K.155, C:H.33, C:H.65 Hydrophobic interactions: C:L.99 Hydrogen bonds: C:S.58, C:A.94

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 6 residues within 4Å: Chain B: G.161, Y.162, R.165 Chain C: G.161, Y.162, R.165 8 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:G.161, C:Y.162, B:Y.162 Water bridges: C:R.165, A:R.165, B:L.163 Salt bridges: C:R.165, B:R.165

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 8 residues within 4Å: Chain A: Y.30, Q.172 Chain B: I.122, L.163, E.170 Chain C: Y.30, E.170, Q.172 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:Q.172, A:Q.172 Water bridges: C:Y.30, B:Y.30, B:N.157, A:Q.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O Rourke, P.E. et al., Crystal Structures of Ispf from Plasmodium Falciparum and Burkholderia Cenocepacia: Comparisons Inform Antimicrobial Drug Target Assessment. Bmc Struct.Biol. (2014)

Release Date

2014-01-08

Peptides

2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE

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